The game don't allow 2 nations to share ownership of a region, although you can have 2 enemy factions in the same region if there is a siege.
So because of that, if we wanted to have some kind of Judea gameplay where the goal was the liberation of Jerusalem after some time (and not at the historical time forcefully), then we had to create a Judea-in-exile government and power base in an adjacent region.
This is obviously not strictly historical. Jews went along rather well with their Greek-flavored occupiers for quite some time. But then as you know, because of some misruling of Antiochius IV a revolt happened in 167 BCE.
Empires is not an historical simulation, it is less historical than the former AGEOD games we did (at AGEOD obviously

). It has strong historical elements, and if we don't have to choose between historicity and gameplay fun, then we do both. If we have to choose, most of the time historicity takes the 2nd row. Plus there are time like for Judea where given how the game rules are done, it is simply not possible to do the perfect historical setting, with some Judea resistance cells within an occupied region.
The game is a load of fun, but you'll get the maximum from it if you don't try to double check that each and every tidbit of gameplay is 100% historical. Another example, the Celts nations can build 4 Nemetons (temple in Celtic). If you manage to build the 4 of them in a single region, then you get vast benefits, attributed to the presence of the Celtic gods. This is done in a way that it might just be the interpretation of the people of the time, that indeed the gods are in the temples. But perhaps not. We don't know. But you get a real gameplay benefit. Is it historical? Certainly not, but it gives a nice gameplay twist that is indeed Celtic-flavored!
AGEOD Team - Makers of Empires, ACW2, WON, EAW, PON, AJE, RUS, ROP, WIA.